Use when the user needs to run GitNexus CLI commands like analyze/index a repo, check status, clean the index, generate a wiki, or list indexed repos. Examples: "Index this repo", "Reanalyze the codebase", "Generate a wiki"

GitNexus CLI Commands Commands below use node .gitnexus/run.cjs <command — the project local runner gitnexus analyze drops next to the index. It auto selects an available runner at call time (global gitnexus , else pnpm dlx , else bunx , else npx ), so no package manager assumption and no global install is required — including on a bun only machine, which has no npm, npx or pnpm at all. Not analyzed yet, or node .gitnexus/run.cjs reports Cannot find module (the gitignored runner is absent — e.g. a fresh clone or git clean )? (Re)generate it with npx gitnexus analyze from the project root, or bunx gitnexus@latest analyze on a bun only machine. On npm 11.x , if npx crashes during install ( node.target is null ), install once with npm i g gitnexus (then gitnexus analyze ), or use bunx gitnexus@latest analyze , or pnpm allow build=@ladybugdb/core allow build=gitnexus allow build=tree sitter dlx gitnexus@latest analyze . See [ 1939](https://github.com/abhigyanpatwari/GitNexus/issues/1939). Commands analyze — Build or refresh the index Run from the project root. This parses all source files, builds the knowledge graph, writes it to .gitnexus/ , and generates CLAUDE.md / AGENTS.md context files. Flag Effect watch Keep a Git repository index current with serialized refreshes debounce <ms Watch quiet period before refresh (default: 300 ms) force Force full re index even if up to date embeddings Enable embedding generation for semantic search (off by default) drop embeddings Drop existing embeddings on rebuild. By default, an analyze without embeddings preserves them. pdg Build the program dependence layers used by explain and pdg query (taint, CDG, and REACHING DEF). spring actuator <path Import opt in Spring Boot Actuator mappings, beans, conditions, configprops, and env snapshots. Forces a full rebuild; unsupported with watch . asyncapi spec <path Read opt in AsyncAPI 3.x documents (directory or single file) and mint Destination nodes from their operations. 2.x is refused, not mapped. Unsupported with watch . When to run: First time in a project, after major code changes, or when gitnexus://repo/{name}/context reports the index is stale. In Claude Code, a PostToolUse hook detects staleness after git commit and git merge and notifies the agent to run analyze — the hook does not run analyze itself, to avoid blocking the agent for up to 120s and risking KuzuDB corruption on timeout. For Spring runtime enrichment, pass a JSON bundle, one endpoint JSON file, or a directory containing endpoint files. Route evidence is authoritative only when runtimeConfirmed === true ; runtimeSource records provenance and may also accompany handler conflict . Env/configprops values are never persisted. Index storage and retention Default location is <repo /.gitnexus/ . Override with environment variables (also documented in README): Env Effect GITNEXUS STORAGE PATH One complete external index directory. Wins if both storage vars are set. GITNEXUS STORAGE ROOT Absolute root; GitNexus creates an isolated <repo basename <12 hex / slot per repository. GITNEXUS CONTENT RETENTION full (default) keeps file text; symbol keeps snippets; none keeps the graph only. list repos , gitnexus://repo/{name}/context , and HTTP GET /api/repos / GET /api/repo expose storagePath , contentRetention , and sourceAvailable . HTTP /api/file and /api/grep return 410 unless retention is full . MCP include content may still return symbol spans when retention is symbol . Use node .gitnexus/run.cjs analyze watch for a long lived local Git repository. It performs an initial analysis, queues scanner admitted file changes, and retries intact failed batches with bounded backoff. Watch refreshes update only the graph: they skip AGENTS.md / CLAUDE.md injection and standard skill installation, so run a one shot analyze when those generated files need updating. Watch rejects one shot or context output flags including force , embedding flags, skills , default branch , skip agents md , skip skills , no stats , self commit , index only , and skip git . It never pulls remotes. Scheduled remote clone/pull is a different command: gitnexus auto sync . Bare gitnexus watch is reserved and does not start either job. Running MCP and serve processes periodically check for a published replacement and reopen it without a restart. MCP checks are throttled to once every five seconds, so a tool call before the next check can briefly use the previous index. status — Check index freshness Shows whether the current repo has a GitNexus index, when it was last updated, and symbol/relationship counts. Use this to check if re indexing is needed. clean — Delete the index Deletes the .gitnexus/ directory and unregisters the repo from the global registry. Use before re indexing if the index is corrupt or after removing GitNexus from a project. Flag Effect force Skip confirmation prompt all Clean all indexed repos, not just the current one wiki — Generate documentation from the graph Generates repository documentation from the knowledge graph using an LLM. HTTP providers require an API key (saved to ~/.gitnexus/config.json on first use). Local CLI providers ( provider cursor claude codex opencode grok ) use your existing CLI login. Flag Effect force Force full regeneration, also required to re generate an existing wiki in a different language provider <name LLM provider: minimax, openai, openrouter, azure, custom, cursor, claude, codex, opencode, or grok (default: minimax). Local CLIs ( cursor , claude , codex , opencode , grok ) use your existing CLI login and skip api key . model <model LLM model (default: MiniMax M3) base url <url LLM API base URL api key <key LLM API key concurrency <n Parallel LLM calls (default: 3) timeout <seconds LLM request timeout in seconds (default: disabled) retries <n Max LLM retry attempts per request (default: 3) lang <lang Output language for generated documentation (e.g. english, chinese, spanish, japanese) gist Publish wiki as a public GitHub Gist list — Show all indexed repos Lists all repositories registered in ~/.gitnexus/registry.json . The MCP list repos tool provides the same information. After Indexing 1. Read gitnexus://repo/{name}/context to verify the index loaded 2. Use the other GitNexus skills ( exploring , debugging , impact analysis , refactoring ) for your task Troubleshooting "Not inside a git repository" : Run from a directory inside a git repo Index is stale after re analyzing : Wait for the next MCP tool call to reopen the published index; this normally takes no more than five seconds Embeddings slow : Omit embeddings (it's off by default) or set OPENAI API KEY for faster API based embedding

gitnexus-cli